Codebase list ctdconverter / 572e9a1
Schema validation is neither mandatory nor default; removing schema/ folder; updated README.md Luis de la Garza 7 years ago
4 changed file(s) with 18 addition(s) and 345 deletion(s). Raw diff Collapse all Expand all
+5
-6
README.md less more
8888 * Purpose: Provide validation of input CTDs against a schema file (i.e, a XSD file).
8989 * Short/long version: `v` / `--validation-schema`
9090 * Required: no.
91 * Taken values: location of the schema.
92 * Default value: `schema/CTD.xsd`.
93
94 CTDs can be validated against a schema. A copy of the most recent `CTD.xsd` is contained in the `schema` folder. However, the master version of the schema can be found under [CTDSchema].
95
96 All input CTDs will automatically be validated against a schema. You can, however, validate against other schema by using this parameter.
91 * Taken values: location of the schema file (e.g., CTD.xsd).
92
93 CTDs can be validated against a schema. The master version of the schema can be found under [CTDSchema].
94
95 If a schema is provided, all input CTDs will be validated against it.
9796
9897 ### Input file(s)
9998
+13
-4
generator.py less more
308308 parser.add_argument("-p", "--hardcoded-parameters", dest="hardcoded_parameters", default=None, required=False,
309309 help="File containing hardcoded values for the given parameters. Run with '-h' or '--help' "
310310 "to see a brief example on the format of this file.")
311 parser.add_argument("-v", "--validation-schema", dest="xsd_location", default="schema/CTD.xsd", required=False,
312 help="Location of the schema to use to validate CTDs. Default value is 'schema/CTD.xsd'")
311 parser.add_argument("-v", "--validation-schema", dest="xsd_location", default=None, required=False,
312 help="Location of the schema to use to validate CTDs.")
313313
314314 # TODO: add verbosity, maybe?
315315 parser.add_argument("-V", "--version", action='version', version=program_version_message)
561561 # first, generate a model
562562 is_converting_multiple_ctds = len(input_files) > 1
563563 parsed_models = []
564 schema = etree.XMLSchema(etree.parse(kwargs["xsd_location"]))
564 schema = None
565 if kwargs["xsd_location"] is not None:
566 try:
567 info("Loading validation schema from %s" % kwargs["xsd_location"], 0)
568 schema = etree.XMLSchema(etree.parse(kwargs["xsd_location"]))
569 except Exception, e:
570 error("Could not load validation schema %s. Reason: %s" % (kwargs["xsd_location"], str(e)), 0)
571 else:
572 info("Validation against a schema has not been enabled.", 0)
565573 for input_file in input_files:
566574 try:
567 validate_against_schema(input_file, schema)
575 if schema is not None:
576 validate_against_schema(input_file, schema)
568577 model = CTDModel(from_file=input_file)
569578 except Exception, e:
570579 error(str(e), 1)
+0
-205
schema/CTD.xsd less more
0 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
1 <!-- Mit XMLSpy v2007 sp1 bearbeitet (http://www.altova.com) von Oliver Kohlbacher (Universität Tübingen) -->
2 <!-- Draft-Version 0.3 -->
3 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
4 <xs:include schemaLocation="Param_1_7_0.xsd" />
5 <xs:element name="tool">
6 <xs:complexType>
7 <xs:all>
8 <xs:element name="description" type="xs:string" minOccurs="0">
9 <xs:annotation>
10 <xs:documentation>One line description of the tool.</xs:documentation>
11 </xs:annotation>
12 </xs:element>
13 <xs:element name="manual" type="xs:string" minOccurs="0">
14 <xs:annotation>
15 <xs:documentation>More detailed description of the tool (about 10 lines).</xs:documentation>
16 </xs:annotation>
17 </xs:element>
18 <xs:element name="citations" type="citationsType" minOccurs="0">
19 <xs:annotation>
20 <xs:documentation />
21 </xs:annotation>
22 </xs:element>
23 <xs:element name="executableName" type="xs:string" minOccurs="0">
24 <xs:annotation>
25 <xs:documentation>Optionally a separate name for the executable can be specified here.</xs:documentation>
26 </xs:annotation>
27 </xs:element>
28 <xs:element name="executablePath" type="xs:anyURI" minOccurs="0">
29 <xs:annotation>
30 <xs:documentation>Contains the path were the tool can be found using either the name element or (if set) the executableName.</xs:documentation>
31 </xs:annotation>
32 </xs:element>
33 <xs:element name="cli" type="cliType" minOccurs="0" />
34 <xs:element name="logs" type="logCollectionType" minOccurs="0" />
35 <xs:element name="relocators" type="relocatorCollectionType" minOccurs="0">
36 <xs:annotation>
37 <xs:documentation>Defines rules to find the output of the tool and move it to the originally desired location.</xs:documentation>
38 </xs:annotation>
39 </xs:element>
40 <xs:element name="PARAMETERS" type="PARAMETERSType" />
41 </xs:all>
42 <xs:attribute name="version" type="xs:string" use="required" />
43 <xs:attribute name="name" use="required">
44 <xs:annotation>
45 <xs:documentation>Name of the tool. Needs to pass following regular expression [A-Za-z0-9_\-]+</xs:documentation>
46 </xs:annotation>
47 <xs:simpleType>
48 <xs:restriction base="xs:string">
49 <xs:pattern value="[A-Za-z0-9_\-]+" />
50 </xs:restriction>
51 </xs:simpleType>
52 </xs:attribute>
53 <xs:attribute name="docurl" type="xs:anyURI">
54 <xs:annotation>
55 <xs:documentation>URL to further documentation (WWW).</xs:documentation>
56 </xs:annotation>
57 </xs:attribute>
58 <xs:attribute name="category" type="xs:string" default="">
59 <xs:annotation>
60 <xs:documentation>The category gives information on the task the associated tool performs. It can be used to categorize different tools in a GUI.</xs:documentation>
61 </xs:annotation>
62 </xs:attribute>
63 <xs:attribute name="ctdVersion" type="versionString" use="required">
64 <xs:annotation>
65 <xs:documentation>Version of the CTD schema.</xs:documentation>
66 </xs:annotation>
67 </xs:attribute>
68 <xs:attribute name="tags" type="xs:string">
69 <xs:annotation>
70 <xs:documentation>List of tags for the tool.</xs:documentation>
71 </xs:annotation>
72 </xs:attribute>
73 </xs:complexType>
74 </xs:element>
75 <xs:complexType name="cliType">
76 <xs:annotation>
77 <xs:documentation>Wraps the information necessary to construct a command line call for the tool.</xs:documentation>
78 </xs:annotation>
79 <xs:sequence>
80 <xs:element name="clielement" type="cliElementType" maxOccurs="unbounded" />
81 </xs:sequence>
82 </xs:complexType>
83 <xs:complexType name="citationsType">
84 <xs:annotation>
85 <xs:documentation>List of citations for the this tool.</xs:documentation>
86 </xs:annotation>
87 <xs:sequence>
88 <xs:element name="citation" type="citationType" maxOccurs="unbounded" />
89 </xs:sequence>
90 </xs:complexType>
91 <xs:complexType name="citationType">
92 <xs:annotation>
93 <xs:documentation>Defines a single citation</xs:documentation>
94 </xs:annotation>
95 <xs:attribute name="doi" type="xs:string">
96 <xs:annotation>
97 <xs:documentation>The Digital Object Identifier for this citation.</xs:documentation>
98 </xs:annotation>
99 </xs:attribute>
100 <xs:attribute name="url" type="xs:anyURI">
101 <xs:annotation>
102 <xs:documentation>A URL for this documentation.</xs:documentation>
103 </xs:annotation>
104 </xs:attribute>
105 </xs:complexType>
106 <xs:complexType name="mappingType">
107 <xs:annotation>
108 <xs:documentation>Defines which ITEM from the parameter part is associated to cliElement.</xs:documentation>
109 </xs:annotation>
110 <xs:attribute name="referenceName" type="xs:string" />
111 <xs:attribute name="referenceID" type="xs:IDREF" />
112 </xs:complexType>
113 <xs:complexType name="cliElementType">
114 <xs:annotation>
115 <xs:documentation>Wraps a single element of a command line call (e.g., the -v flag for verbosity) and it's associated arguments. To model a non-option argument just leave the optionIdentifier empty.</xs:documentation>
116 </xs:annotation>
117 <xs:sequence>
118 <xs:element name="mapping" type="mappingType" minOccurs="0" maxOccurs="unbounded">
119 <xs:annotation>
120 <xs:documentation>The mapping defines the association between the cliElement and the PARAM part. Note: If the mapped parameter is boolean, the optionIdentifier will be added to the CLI only if the mapped value is true.</xs:documentation>
121 </xs:annotation>
122 </xs:element>
123 </xs:sequence>
124 <xs:attribute name="optionIdentifier" type="xs:string" use="optional">
125 <xs:annotation>
126 <xs:documentation>A string used to prefix any associated values (e.g., "-v" for a boolean flag to turn on verbosity).</xs:documentation>
127 </xs:annotation>
128 </xs:attribute>
129 <xs:attribute name="isList" type="xs:boolean" use="optional">
130 <xs:annotation>
131 <xs:documentation>A boolean attribute indicating whether or not the given cliElement can be expended to occur more then once on the command line.</xs:documentation>
132 </xs:annotation>
133 </xs:attribute>
134 <xs:attribute name="required" type="xs:boolean" use="optional">
135 <xs:annotation>
136 <xs:documentation>Defines if the cliElement is required to build the full command line, i.e., if required is set to false and the mapped parameter was not set the complete element will not be used on the final cli.</xs:documentation>
137 </xs:annotation>
138 </xs:attribute>
139 </xs:complexType>
140 <xs:complexType name="logCollectionType">
141 <xs:annotation>
142 <xs:documentation>Wraps the log informations from the call of the tool.</xs:documentation>
143 </xs:annotation>
144 <xs:sequence>
145 <xs:element name="log" type="logType" maxOccurs="unbounded">
146 <xs:annotation>
147 <xs:documentation>...</xs:documentation>
148 </xs:annotation>
149 </xs:element>
150 </xs:sequence>
151 </xs:complexType>
152 <xs:complexType name="logType">
153 <xs:annotation>
154 <xs:documentation>Wraps the log informations from the call of the tool.</xs:documentation>
155 </xs:annotation>
156 <xs:sequence>
157 <xs:element name="executionWarnings" type="xs:string" minOccurs="0" maxOccurs="unbounded">
158 <xs:annotation>
159 <xs:documentation>...</xs:documentation>
160 </xs:annotation>
161 </xs:element>
162 <xs:element name="executionErrors" type="xs:string" minOccurs="0" maxOccurs="unbounded">
163 <xs:annotation>
164 <xs:documentation>...</xs:documentation>
165 </xs:annotation>
166 </xs:element>
167 <xs:element name="executionMessage" type="xs:string" minOccurs="0" maxOccurs="unbounded" />
168 </xs:sequence>
169 <xs:attribute name="executionTimeStart" type="xs:dateTime" use="required" />
170 <xs:attribute name="executionTimeStop" type="xs:dateTime" use="required" />
171 <xs:attribute name="executionStatus" type="xs:int" use="required" />
172 </xs:complexType>
173 <xs:complexType name="logMessageType">
174 <xs:sequence>
175 <xs:element name="logMessage" type="xs:string" minOccurs="0" maxOccurs="unbounded" />
176 </xs:sequence>
177 <xs:attribute name="NODEref" type="xs:IDREF" />
178 </xs:complexType>
179 <xs:complexType name="relocatorCollectionType">
180 <xs:sequence>
181 <xs:element name="relocator" type="relocatorType" />
182 </xs:sequence>
183 </xs:complexType>
184 <xs:complexType name="relocatorType">
185 <xs:sequence>
186 <xs:annotation>
187 <xs:documentation>Defines a relocation rule using a pattern to find the file and the targeted output file where the found file should be moved to.</xs:documentation>
188 </xs:annotation>
189 <xs:element name="reference" type="xs:string">
190 <xs:annotation>
191 <xs:documentation>The referenced parameter which should be relocated.</xs:documentation>
192 </xs:annotation>
193 </xs:element>
194 <xs:element name="location" type="xs:string">
195 <xs:annotation>
196 <xs:documentation>The location of the output file defined using following variables:
197 %TEMP% - the temporary directory while executing
198 %PWD% - the working directory while executing
199 %BASENAME[PARAM]% - the base name of PARAM</xs:documentation>
200 </xs:annotation>
201 </xs:element>
202 </xs:sequence>
203 </xs:complexType>
204 </xs:schema>⏎
+0
-130
schema/Param_1_7_0.xsd less more
0 <?xml version="1.0" encoding="UTF-8"?>
1 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
2 <xs:element name="PARAMETERS" type="PARAMETERSType">
3 <xs:annotation>
4 <xs:documentation>Main parameters node.</xs:documentation>
5 </xs:annotation>
6 </xs:element>
7 <xs:complexType name="PARAMETERSType">
8 <xs:sequence>
9 <xs:group ref="ITEMS" minOccurs="0" maxOccurs="unbounded" />
10 <xs:element name="NODE" type="NODEType" minOccurs="0" maxOccurs="unbounded" />
11 </xs:sequence>
12 <xs:attribute name="version" type="versionString" />
13 </xs:complexType>
14 <xs:complexType name="AbstractITEMType" abstract="true">
15 <xs:attribute name="name" use="required">
16 <xs:simpleType>
17 <xs:restriction base="xs:string">
18 <xs:minLength value="1" />
19 </xs:restriction>
20 </xs:simpleType>
21 </xs:attribute>
22 <xs:attribute name="type" type="PossibleITEMType" use="required">
23 <xs:annotation>
24 <xs:documentation>The type of the specified ITEM. Either input or output.</xs:documentation>
25 </xs:annotation>
26 </xs:attribute>
27 <xs:attribute name="description" type="xs:string" default="" />
28 <xs:attribute name="short_description" type="xs:string">
29 <xs:annotation>
30 <xs:documentation>A short description of the parameter.</xs:documentation>
31 </xs:annotation>
32 </xs:attribute>
33 <xs:attribute name="tags" type="xs:string" default="false">
34 <xs:annotation>
35 <xs:documentation>Additional annotations of the parameter incl. required, advanced, thread, debug, internal, file-type-override, log</xs:documentation>
36 </xs:annotation>
37 </xs:attribute>
38 <xs:attribute name="restrictions" type="xs:string" default="" />
39 <xs:attribute name="supported_formats" type="xs:string" default="false">
40 <xs:annotation>
41 <xs:documentation>Defines the expected file types. Only valid for input-file, output-file, input-prefix, and output-prefix parameters.</xs:documentation>
42 </xs:annotation>
43 </xs:attribute>
44 <xs:attribute name="required" type="xs:boolean" default="false">
45 <xs:annotation>
46 <xs:documentation>Deprecated, embed as tag into tags attribute. Will be removed in v2.0.0 of the schema.</xs:documentation>
47 </xs:annotation>
48 </xs:attribute>
49 <xs:attribute name="advanced" type="xs:boolean" default="false">
50 <xs:annotation>
51 <xs:documentation>Deprecated, embed as tag into tags attribute. Will be removed in v2.0.0 of the schema.</xs:documentation>
52 </xs:annotation>
53 </xs:attribute>
54 </xs:complexType>
55 <xs:complexType name="ITEMLISTType">
56 <xs:complexContent>
57 <xs:extension base="AbstractITEMType">
58 <xs:sequence>
59 <xs:element name="LISTITEM" type="LISTITEMType" minOccurs="0" maxOccurs="unbounded" />
60 </xs:sequence>
61 </xs:extension>
62 </xs:complexContent>
63 </xs:complexType>
64 <xs:complexType name="LISTITEMType">
65 <xs:attribute name="value" use="required" />
66 </xs:complexType>
67 <xs:complexType name="ITEMType">
68 <xs:complexContent>
69 <xs:extension base="AbstractITEMType">
70 <xs:attribute name="value" type="xs:string" use="required">
71 <xs:annotation>
72 <xs:documentation>The actual value of the parameter.</xs:documentation>
73 </xs:annotation>
74 </xs:attribute>
75 <xs:attribute name="default" type="xs:string" use="optional">
76 <xs:annotation>
77 <xs:documentation>If available, the default value of the given parameter.</xs:documentation>
78 </xs:annotation>
79 </xs:attribute>
80 </xs:extension>
81 </xs:complexContent>
82 </xs:complexType>
83 <xs:simpleType name="PossibleITEMType">
84 <xs:annotation>
85 <xs:documentation>Defines the possible types available in the type attribute of ITEM and ITEMLIST.</xs:documentation>
86 </xs:annotation>
87 <xs:restriction base="xs:string">
88 <xs:enumeration value="int" />
89 <xs:enumeration value="double" />
90 <xs:enumeration value="float" />
91 <xs:enumeration value="string" />
92 <xs:enumeration value="int-pair" />
93 <xs:enumeration value="double-pair" />
94 <xs:enumeration value="input-prefix" />
95 <xs:enumeration value="output-prefix" />
96 <xs:enumeration value="input-file" />
97 <xs:enumeration value="output-file" />
98 <xs:enumeration value="bool" />
99 </xs:restriction>
100 </xs:simpleType>
101 <xs:group name="ITEMS">
102 <xs:choice>
103 <xs:element name="ITEM" type="ITEMType" />
104 <xs:element name="ITEMLIST" type="ITEMLISTType" />
105 </xs:choice>
106 </xs:group>
107 <xs:complexType name="NODEType">
108 <xs:annotation>
109 <xs:documentation />
110 </xs:annotation>
111 <xs:choice minOccurs="0" maxOccurs="unbounded">
112 <xs:group ref="ITEMS" />
113 <xs:element name="NODE" type="NODEType" />
114 </xs:choice>
115 <xs:attribute name="name" use="required">
116 <xs:simpleType>
117 <xs:restriction base="xs:string">
118 <xs:minLength value="1" />
119 </xs:restriction>
120 </xs:simpleType>
121 </xs:attribute>
122 <xs:attribute name="description" type="xs:string" default="" />
123 </xs:complexType>
124 <xs:simpleType name="versionString">
125 <xs:restriction base="xs:string">
126 <xs:pattern value="\d+\.\d+(\.\d+)?" />
127 </xs:restriction>
128 </xs:simpleType>
129 </xs:schema>⏎